... | ... | @@ -12,15 +12,22 @@ phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map -m |
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This procedure generates three files:
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- pdb3j5p_4locscale.pdb (shifted) PDB model with same P1 unit cell as map
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- `pdb3j5p_4locscale.mrc` __Reference model map__
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- `emd_5778_full_4locscale.mrc` __(shifted) original reconstruction__
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- `pdb3j5p_4locscale.pdb` __(shifted) PDB model with same P1 unit cell as EM map__
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- `pdb3j5p_4locscale.mrc` __(shifted) reference model map__
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- `emd_5778_full_4locscale.mrc` __(shifted) original reconstruction__
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<br>
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The two MRC maps are to be used for input in the LocScale procedure.
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The two MRC maps produced (`pdb3j5p_4locscale.mrc` and `emd_5778_full_4locscale.mrc`) are to be used for input in the LocScale procedure.
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By default structure factors from the model are computed to Nyquist frequency. This is the preferred procedure for sharpening using LocScale.
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A different resolution cut-off can be supplied using the ```-dmin``` flag. See
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<hr>
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**NOTE**:
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CCTBX/CCP4 follow the ZXY convention for map axis order, whereas most EM programs follow XYZ. This will mostly not have any consequences for visualization, but it may cause issues in further processing.
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##### It is preferable to proceed in XYZ convention, please see [here](map_permute_axis_order).
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<hr>
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<br>
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By default structure factors from the model are computed to Nyquist frequency. This is the preferred procedure for sharpening using LocScale. A different resolution cut-off can be supplied using the ```-dmin``` flag, e.g.
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```
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phenix.python prepare_locscale_input.py -mc pdb3j5p.pdb -em emd_5778_full.map -dmin 4.0
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... | ... | @@ -30,13 +37,11 @@ See [```prepare_locscale_input.py```](prepare_locscale_input.py) script for furt |
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<br>
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LocScale maps can be computed using any source of reference maps for scaling. If you prefer to use your own workflow to generate reference model maps, we do recommend to make sure your map complies with the [following procedure](model_map_generation_from_arbitrary_files).
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#### Note:
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CCTBX/CCP4 follow the ZYX convention for map axis order, whereas most EM programs follow XYZ. This will mostly not have any consequences for visualization, but it may cause issues in further processing. If you prefer to process in the XYZ convention please see [here](map_permute_axis_order).
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<br>
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[//]: # (#### __PLEASE download the following [electron form factor table](electron_scattering.py) for use with pdb2map.py.__)
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References:
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##### References:
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[[1]](https://doi.org/10.1101/121913) Jakobi et al. bioRxiv 121913 (2017)
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[[2]](https://www.nature.com/nature/journal/v504/n7478/full/nature12822.html) Liao et al., _Nature_ __504__:107-112 (2013)
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[[3]](http://challenges.emdatabank.org/?q=model_challenge) EMDB Model Challenge 2015/2016 |
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\ No newline at end of file |